[Bioc-devel] Reopen cfTools issue #2608
Hi, I am the maintainer of cfTools issue #2608. I submitted it last year but didn't have many updates then. This issue has been closed. Now I have modified the package and am ready to submit it again. Could you please reopen the issue? Many thanks! Best, Ran [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] updating pathwayPCA: "permission denied (publickey)"
Thank you Prof. MacDonald. The solution ended up being slightly different than we had anticipated, but I'm including it below should any other users have similar difficulties. TL;DR: RStudio Terminal can't find my SSH key (despite being listed in the RStudio Global Options), but Git Bash can. Solution: push upstream via Git Bash. Long version: I use Git via the Terminal in RStudio rather than through more traditional means. As of last year, the home directory (~/) on Windows for an RStudio Terminal is different than the home directory for the rest of the computer. This issue is documented here (https://community.rstudio.com/t/git-bash-uses-different-home-directory-in-rstudio-2022-12-0-on-windows/155508), but has not yet been resolved. For me, this means that I had the correct RSA key according to Git Bash (~/ = C:/Users/godom/) and RStudio Global Options (~/ = C:/Users/godom/), but not for the RStudio Terminal which I used in my attempts to perform a git push (~/ = C:/Users/godom/Documents/, which obviously doesn't have the expected .ssh/ folder). -Original Message- From: Bioc-devel On Behalf Of James W. MacDonald Sent: Thursday, February 9, 2023 3:50 PM To: Gabriel Odom ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] updating pathwayPCA: "permission denied (publickey)" Note: This message originated from outside the FIU Faculty/Staff email system. That looks like you have the wrong RSA key. You should be able to check which key you are using by logging in here: https://urldefense.com/v3/__https://git.bioconductor.org/BiocCredentials/login/__;!!FjuHKAHQs5udqho!LGpeGB2VKDnOCR9x6ZTjbGZGzrsTdPAf9rpYI4UGgwNWl2StQ8BMlhIRUBnu9TX2pHK5nP0VaNJhbbiRsI8$ -Original Message- From: Bioc-devel On Behalf Of Gabriel Odom Sent: Thursday, February 9, 2023 1:56 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] updating pathwayPCA: "permission denied (publickey)" Dear BioC-Devel folks, My package, pathwayPCA, had an error in the vignettes which I've just fixed. It's been a few years since my last bug fix, and I don't know what I'm doing wrong. When I use "git push upstream master", I see "mailto:g...@git.bioconductor.org: Permission denied (publickey)." Using "git remote -v" shows "upstream mailto:g...@git.bioconductor.org:packages/pathwayPCA.git (push)" (and pull). Am I missing something simple? Best, Gabriel Gabriel J. Odom, PhD, ThD Assistant Professor Department of Biostatistics Stempel College of Public Health Florida International University Office: (305) 348-5486 Email: gabriel.o...@fiu.edu ___ Bioc-devel@r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!lgUqo10igxIGCi2Ltk5ROGKBk4zpJU2-R56q0s-o57z8DPMtm03l92N486lSHV_-Luj2SloQg9_4$ ___ Bioc-devel@r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!FjuHKAHQs5udqho!LGpeGB2VKDnOCR9x6ZTjbGZGzrsTdPAf9rpYI4UGgwNWl2StQ8BMlhIRUBnu9TX2pHK5nP0VaNJhouP-go4$ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Single Package Builder package dependency issue
We recently updated R on the devel builders. Some of the recent updates have temporarily caused issues with finding package dependencies on the Single Package Builder for new submission. We are aware of the issue and are working on a fix. We are sorry for the inconvenience and will have it remedied soon Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] download stats not accessible
While I too wondered why the OP mentions unavailability "for months", now re-reading the OP's email, may be they meant "for months" granularity which is (now temporarily un)available! :D Cheers, Sarvesh On Mon, 20 Mar 2023 at 16:50, Hervé Pagès wrote: > Not for months, only since last week. They should be back in the next > 12-18 hours. Thanks for reporting this. > > Cheers, > > H. > > On 19/03/2023 11:00, Luo Weijun wrote: > > Dear BioC team, > > I noticed that download stats for BioC packages are not accessible for > months: > > https://bioconductor.org/packages/stats/bioc/pathview/ > > https://bioconductor.org/packages/stats/bioc/BiocGenerics/ > > > > can you check on this? thanks. > > Weijun Luo > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- thanks! -Sarvesh Q: Why is this email five sentences or less? A: http://five.sentenc.es [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] download stats not accessible
Not for months, only since last week. They should be back in the next 12-18 hours. Thanks for reporting this. Cheers, H. On 19/03/2023 11:00, Luo Weijun wrote: Dear BioC team, I noticed that download stats for BioC packages are not accessible for months: https://bioconductor.org/packages/stats/bioc/pathview/ https://bioconductor.org/packages/stats/bioc/BiocGenerics/ can you check on this? thanks. Weijun Luo -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Packages failing on macOS build system - recent updates to the build system?
Johannes, Thanks for reporting this. It should improve in the next build report. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Rainer Johannes Sent: Monday, March 20, 2023 6:44 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Packages failing on macOS build system - recent updates to the build system? ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Bioc core, after checking some build reports for a set of packages it seems that many are failing due some recent updates with the macOS builder. The common theme seems to be that for these packages (CRAN) dependencies "magick" and "rsvg" are not available on macOS. Just wanted to give a heads up to please look maybe into this. cheers, jo --- Johannes Rainer, PhD Eurac Research Institute for Biomedicine Via A.-Volta 21, I-39100 Bolzano, Italy email: johannes.rai...@eurac.edu github: jorainer mastodon: jorai...@fosstodon.org [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=NM3U9HAHfVzAWpSuLY4aJgQr9DebXN7zAPBYE0J2YpsKnE8oCitCeoWzRwrpiX5L=hqPoWN-D6jh3kIFn41OlxO-XMf-Np2PVx_oMgDMgE2Q= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Packages failing on macOS build system - recent updates to the build system?
Dear Bioc core, after checking some build reports for a set of packages it seems that many are failing due some recent updates with the macOS builder. The common theme seems to be that for these packages (CRAN) dependencies "magick" and "rsvg" are not available on macOS. Just wanted to give a heads up to please look maybe into this. cheers, jo --- Johannes Rainer, PhD Eurac Research Institute for Biomedicine Via A.-Volta 21, I-39100 Bolzano, Italy email: johannes.rai...@eurac.edu github: jorainer mastodon: jorai...@fosstodon.org [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
